Fanconi anemia complementation group protein E (FANCE), which is a member of FA family, plays a critical role in DNA interstrand crosslink (ICL) repair and contributes to progression of tumor. We used series of bioinformatics to predict and analyze the properties of human FANCE, involving homology, physicochemical property, hydrophobicity, signal peptide, subcellular localization, protein structure, protein-protein interaction, B/T cell epitopes and its correlation with tumor. FANCE was hydrophobic protein, without signal peptide and transmembrane region, mainly distributed in nucleus and cytoplasm. It showed being high conserved in evolution, of which secondary structure was characterized as α-helices and random coils, and had 2 N-glycosylation, 9 O-glycosylation and 48 phosphorylation sites. FANCE also could interact with FANCM, FANCD2, FANCC etc., and had many potential B/T cell epitopes and 17 antigenic determinants. FANCE was lowly expressed in LAML and SKCM, low FANCE expression reduced overall patient survival in SKCM. This study provides a theoretical basis for further researching the molecular mechanism of FANCE in tumors, which may offer potential as a novel therapeutic target.